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New versions of picard-private, sam and picard jars for TileCovariate and regeneration of NM tag 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2456 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
alecw 2009-12-28 22:18:55 +00:00
parent d4ee999ef9
commit b5e5e27225
8 changed files with 6 additions and 7 deletions
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3
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolTest.java
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@ -32,8 +32,6 @@ import java.io.FileNotFoundException;
public class ReferenceOrderedDataPoolTest extends BaseTest { public class ReferenceOrderedDataPoolTest extends BaseTest {
private static File sequenceFile = new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta");
private ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = null; private ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = null;
private final GenomeLoc testSite1 = GenomeLocParser.createGenomeLoc("chrM",10); private final GenomeLoc testSite1 = GenomeLocParser.createGenomeLoc("chrM",10);
@ -42,6 +40,7 @@ public class ReferenceOrderedDataPoolTest extends BaseTest {
@BeforeClass @BeforeClass
public static void init() throws FileNotFoundException { public static void init() throws FileNotFoundException {
File sequenceFile = new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta");
GenomeLocParser.setupRefContigOrdering(new IndexedFastaSequenceFile(sequenceFile)); GenomeLocParser.setupRefContigOrdering(new IndexedFastaSequenceFile(sequenceFile));
TabularROD.setDelimiter(TabularROD.DEFAULT_DELIMITER, TabularROD.DEFAULT_DELIMITER_REGEX); TabularROD.setDelimiter(TabularROD.DEFAULT_DELIMITER, TabularROD.DEFAULT_DELIMITER_REGEX);
} }

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settings/repository/edu.mit.broad/picard-private-parts-1194.jar → settings/repository/edu.mit.broad/picard-private-parts-1198.jar
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settings/repository/edu.mit.broad/picard-private-parts-1194.xml → settings/repository/edu.mit.broad/picard-private-parts-1198.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="edu.mit.broad" module="picard-private-parts" revision="1194" status="integration" publication="20091223171200" /> <info organisation="edu.mit.broad" module="picard-private-parts" revision="1198" status="integration" publication="20091228124200" />
</ivy-module> </ivy-module>

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settings/repository/net.sf/picard-1.11.221.jar → settings/repository/net.sf/picard-1.11.225.jar
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settings/repository/net.sf/picard-1.11.221.xml → settings/repository/net.sf/picard-1.11.225.xml
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@ -1,3 +1,3 @@
<ivy-module version="1.0"> <ivy-module version="1.0">
<info organisation="net.sf" module="picard" revision="1.11.221" status="release" /> <info organisation="net.sf" module="picard" revision="1.11.225" status="release" />
</ivy-module> </ivy-module>

3
settings/repository/net.sf/sam-1.11.221.xml
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@ -1,3 +0,0 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.11.221" status="release" />
</ivy-module>

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settings/repository/net.sf/sam-1.11.221.jar → settings/repository/net.sf/sam-1.11.225.jar
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settings/repository/net.sf/sam-1.11.225.xml 100644
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@ -0,0 +1,3 @@
<ivy-module version="1.0">
<info organisation="net.sf" module="sam" revision="1.11.225" status="release" />
</ivy-module>